convert2bed.py

convert2bed.csv2bed(csv, bed=None)

Convert a *.csv file output from allelecounter.py into a *.bed file

convert2bed.gtf2bed(gtf, bed=None)

Convert a *.gtf file into a *.bed file

Note: discard everything except exons

convert2bed.vcf2bed(vcf, bed=None, MIN_TOTAL_COUNT=10, MIN_ALLELE_COUNT=1)

Convert a *.vcf file output from bcftools::call into a *.bed file

MIN_TOTAL_COUNT specifies the minimum number of high quality reads for a candidate to be retained

MIN_ALLELE_COUNT sets a lower limit on the read depth of the minor allele